SMTL ID : 1uxi.1

Large improvement in the thermal stability of a tetrameric malate dehydrogenase by single point mutations at the dimer-dimer interface

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-tetramer

Ligands

4 x NAD: NICOTINAMIDE-ADENINE-DINUCLEOTIDE(Non-covalent)

NAD.1: 30 residues within 4Å: Chain A: I.8, G.9, A.10, G.11, F.12, V.13, L.32, D.33, I.34, V.35, Y.65, T.77, S.78, G.79, A.80, P.81, L.91, N.95, I.98, C.102, V.118, N.119, N.120, L.122, Q.143, L.147, H.175, A.225, P.229 Ligands: FUM.2 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:V.13, A:V.118, A:L.147, A:P.229 Hydrogen bonds: A:A.10, A:F.12, A:V.13, A:I.34, A:G.79, A:A.80, A:N.95, A:N.120, A:N.120, A:Q.143 Water bridges: A:G.11, A:G.14, A:Y.65 NAD.3: 32 residues within 4Å: Chain B: I.8, G.9, A.10, G.11, F.12, V.13, L.32, D.33, I.34, V.35, Y.65, T.77, S.78, G.79, A.80, P.81, L.91, N.95, I.98, C.102, V.118, N.119, N.120, L.122, Q.143, A.144, L.147, H.175, S.224, A.225, P.229 Ligands: FUM.4 17 PLIP interactions: 17 interactions with chain B Hydrophobic interactions: B:V.13, B:V.118, B:L.147, B:P.229 Hydrogen bonds: B:A.10, B:F.12, B:V.13, B:I.34, B:G.79, B:A.80, B:N.95, B:V.118, B:N.120, B:N.120 Water bridges: B:G.11, B:Y.65, B:S.224 NAD.6: 30 residues within 4Å: Chain C: I.8, G.9, A.10, G.11, F.12, V.13, L.32, D.33, I.34, V.35, Y.65, T.77, S.78, G.79, A.80, P.81, L.91, N.95, I.98, C.102, V.118, N.119, N.120, L.122, Q.143, L.147, H.175, A.225, P.229 Ligands: FUM.7 18 PLIP interactions: 18 interactions with chain C Hydrophobic interactions: C:V.13, C:V.118, C:L.147, C:P.229 Hydrogen bonds: C:A.10, C:F.12, C:V.13, C:I.34, C:Y.65, C:G.79, C:A.80, C:N.95, C:N.120, C:N.120, C:Q.143 Water bridges: C:G.11, C:G.14, C:Y.65 NAD.8: 32 residues within 4Å: Chain D: I.8, G.9, A.10, G.11, F.12, V.13, L.32, D.33, I.34, V.35, Y.65, T.77, S.78, G.79, A.80, P.81, L.91, N.95, I.98, C.102, V.118, N.119, N.120, L.122, Q.143, A.144, L.147, H.175, S.224, A.225, P.229 Ligands: FUM.9 18 PLIP interactions: 18 interactions with chain D Hydrophobic interactions: D:V.13, D:V.118, D:L.147, D:P.229 Hydrogen bonds: D:A.10, D:F.12, D:V.13, D:I.34, D:Y.65, D:G.79, D:A.80, D:N.95, D:V.118, D:N.120, D:N.120 Water bridges: D:G.11, D:Y.65, D:S.224

4 x FUM: FUMARIC ACID(Non-covalent)

FUM.2: 10 residues within 4Å: Chain A: R.82, R.88, N.120, L.147, R.151, H.175, G.213, V.217, S.224 Ligands: NAD.1 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:N.120, A:S.224, A:S.224 Water bridges: A:V.217 Salt bridges: A:R.82, A:R.88, A:R.88, A:R.151, A:H.175 FUM.4: 10 residues within 4Å: Chain B: R.82, R.88, N.120, L.147, R.151, H.175, G.213, V.217, S.224 Ligands: NAD.3 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:N.120, B:S.224, B:S.224 Water bridges: B:V.217 Salt bridges: B:R.82, B:R.88, B:R.88, B:R.151, B:H.175 FUM.7: 10 residues within 4Å: Chain C: R.82, R.88, N.120, L.147, R.151, H.175, G.213, V.217, S.224 Ligands: NAD.6 9 PLIP interactions: 9 interactions with chain C Hydrogen bonds: C:N.120, C:S.224, C:S.224 Water bridges: C:V.217 Salt bridges: C:R.82, C:R.88, C:R.88, C:R.151, C:H.175 FUM.9: 10 residues within 4Å: Chain D: R.82, R.88, N.120, L.147, R.151, H.175, G.213, V.217, S.224 Ligands: NAD.8 9 PLIP interactions: 9 interactions with chain D Hydrogen bonds: D:N.120, D:S.224, D:S.224 Water bridges: D:V.217 Salt bridges: D:R.82, D:R.88, D:R.88, D:R.151, D:H.175

2 x NA: SODIUM ION(Non-functional Binders)

NA.5: 3 residues within 4Å: Chain B: T.187 Chain D: T.187 Ligands: NA.10 No protein-ligand interaction detected (PLIP) NA.10: 3 residues within 4Å: Chain B: T.187 Chain D: T.187 Ligands: NA.5 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bjork, A. et al., Large Improvement in the Thermal Stability of a Tetrameric Malate Dehydrogenase by Single Point Mutations at the Dimer-Dimer Interface. J.Mol.Biol. (2004)

Release Date

2004-08-26

Peptides

MALATE DEHYDROGENASE: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

MALATE DEHYDROGENASE

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